- Download the code:
git clone https://github.com/tschuelia/RAxML-NG-comparison.git
- If you don't have miniconda already, install it according to the instructions [here] (https://docs.conda.io/en/latest/miniconda.html#installing)
- Solving the environment using conda is very slow, so I recommend you to use [mamba] (https://github.com/mamba-org/mamba) instead. You can install mamba using conda:
conda install mamba
- Create a new conda environment using the provided
environment.yml
file:mamba env create -f environment.yml
- Activate the conda environment:
conda activate comparison
- Get all RAxML-NG versions you want to test ready to use.
-
Adjust the
config.yaml
file to your needs. The comments in theconfig.yaml
will guide you. -
Do a snakemake dry run to make sure everything works as expected:
snakemake -n -p
This will print all jobs that Snakemake will do.
-
Run the pipeline
snakemake --cores [number of cores*] -k -p
* you can either manually set a number of cores, or you can set
--cores all
and Snakemake will use all cores your system has.Running the pipeline on a cluster is a bit more difficult, especially when we want to run it on multiple nodes. You can find detailed instructions on how to setup snakemake on a slurm cluster here.
-
Once the pipeline ran successfully, you can have a look at the results using an interactive Dash plotting website. You have to start the dash server manually:
python plots/index.py
-
If you ran the pipeline on you laptop, you can directly open
http://127.0.0.1:8050/
in your browser. In case you ran it on a remote server you first have to do port forwarding to view the website:ssh -L 8050:localhost:8050 [address of the server]